Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic Quantification of Lysine Acetylation in mouse hippocampus

ABSTRACT: Major depressive disorder (MDD) is a leading cause of disability around the world and contributes greatly to the global burden of disease. Mounting evidence suggests that gut microbiota dysbiosis may be involved in the pathophysiology of MDD through the microbiota–gut–brain axis. Recent research suggests that epigenetic modifications might relate to depression. However, our knowledge of the role of epigenetics in host–microbe interactions remains limited. In the present study, we used a combination of affinity enrichment and high-resolution liquid chromatography tandem mass spectrometry analysis to identify hippocampal acetylated proteins in germ-free(GF) and specific pathogen-free(SPF) mice. In total, 986 lysine acetylation sites in 543 proteins were identified, of which 747 sites in 427 proteins were quantified. Motif analysis identified several conserved sequences surrounding the acetylation sites, including D*Kac, DKac, KacY, KacD, and D**Kac. Gene ontology annotations revealed that these differentially expressed acetylated proteins were involved in multiple biological functions and mainly located in mitochondria. In addition, pathway enrichment analysis showed that oxidative phosphorylation and the tricarboxylic acid (TCA) cycle II (eukaryotic), both of which are exclusively localized to the mitochondria, were the primarily disturbed functions. Taken together, this study indicates that lysine acetylation changes may play a pivotal role in the mitochondrial dysfunction by which gut microbiota regulate brain function and behavioral phenotypes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Yu Ying

LAB HEAD: xie peng

PROVIDER: PXD022577 | Pride | 2021-03-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1_1.raw	Raw
	2_1.raw	Raw
	3_1.raw	Raw
	4_1.raw	Raw
	5_1.raw	Raw

Items per page:

1 - 5 of 10

Similar Datasets

Metaproteomic analysis of cecal contents from healthy mice versus mice with DSS-induced colitis

Project description:The gut microbiota influences host epigenetics by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-CoA, a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.

2022-12-11 | PXD026959 | Pride

Transcriptomic and epigenomic analysis of germ-free and colitic mice

2022-12-12 | GSE179233 | GEO

LNU Synechococcus genome sequencing

Project description:Synechococcus KAC 102, KAC 105, KAC 106, KAC 108 and KAC 114 genome sequencing

| PRJEB70728 | ENA

First proteomic analysis of lysine acetylation on extensive functions in Solenopsis invicta Buren

Project description:Lysine acetylation (Kac) plays a critical role in the regulation of a great deal of important cellular processes. However, little is known about Kac in Solenopsis invicta, which is one of the 100 most dangerous invasive species in the world. Lysine acetylome in S. invicta was evaluated for the first time in this study. Altogether, 2387 Kac sites were tested in 992 proteins. The prediction of subcellular localization indicated that most identified proteins were located in cytoplasm, mitochondria and nucleus. The enriched Kac site motifs included Kac H, Kac Y, Kac G, Kac F, Kac T, and Kac W. H, Y, F, and W were of frequent occurrence at the +1 position, whereas G, Y and T were of frequent occurrence at the –1 position. Based on cellular component, acetylated proteins were enriched in cytoplasmic part, mitochondrial matrix, and cytosolic ribosome. Furthermore, 25 pathways were detected to be significantly enriched. Interestingly, arginine and proline metabolism as well asphagosome, which were related to immunity, contained several Kac proteins. Acetylation or deacetylation of the proline and phagosome proteins may adjust the protein function, which may be why S. invicta was highly immune. As for interaction network investigation, diverse interactions were adjusted by Kac. Our study of lysine acetylome supplies abundant information for function analysis of reversible Kac in the growth and development of S. invicta and other Hymenoptera insects. Confirming the functions of Kac target proteins may be useful to design specific and effective drugs to prevent and control this dangerous invasive species.

2020-12-02 | PXD019033 | Pride

Analysis of gut microbiota by pyrosequencing of 16S rRNA gene in F344 rats

Project description:Chronic acid suppression by proton pump inhibitor (PPI) has been hypothesized to alter the gut microbiota via a change in intestinal pH. To evaluate the changes in gut microbiota composition by long-term PPI treatment. Twenty-four week old F344 rats were fed with (n = 5) or without (n = 6) lansoprazole (PPI) for 50 weeks. Then, profiles of luminal microbiota in the terminal ileum were analyzed. Pyrosequencing for 16S rRNA gene was performed by genome sequencer FLX (454 Life Sciences/Roche) and analyzed by metagenomic bioinformatics.

2015-04-14 | E-GEOD-67800 | biostudies-arrayexpress

The acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens

Project description:Protein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes including cell cycle regulation, metabolic pathways, enzymatic activities and protein interactions. Brenneria nigrifluens is the pathogen of shallow bark canker of walnut trees and can cause serious disease on walnut trees. Up to now, it is little known about the roles of lysine acetylation in the plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high-resolution LC-MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicate that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac and L*Kac, were identified in this bacterium. Protein interaction network analysis indicates that all kinds of interactions are modulated by protein lysine acetylation. Overall, 14 acetylated proteins are related to the virulence of B. nigrifluens.

2019-09-30 | PXD014046 | Pride

FGFP and TR-MDD shotgun sequencing samples (N=157)

Project description:Study exploring the neuroactive potential of the human gut microbiota in relation to quality of life and depression. This dataset includes shotgun sequenced samples from the FGFP (Flemish Gut Flora Project: N=150) and TR-MDD (Treatment-Resistant Major Depression Disorder: N=7). Samples were provided by volunteers from the Flanders region in Belgium, and the dataset is balanced for age, gender, and stool consistency.

| EGAS00001003298 | EGA

Protein acetylation landscape of developing rice anthers

Project description:Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification, playing important biological roles in many organisms.Here, we reported results from a proteomic investigation to detect KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during rice anther development and meiosis. We identified a total of 1,354 KAC sites in 676 proteins.

2019-03-06 | PXD007986 | Pride

Global Proteomic Analysis of Lysine acetylation in Fusarium oxysporum

Project description:Lysine acetylation (Kac), a discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Fusarium oxysporumis a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kac are unknown in Fusarium oxysporumr any other plant fungal pathogens. Here, we comprehensively evaluated the acetylation proteome ofFusarium oxysporum .

2021-09-09 | PXD020479 | Pride

Lysine acetylation in human fecal microbiome

Project description:This study characterized the lysine acetylome in human gut microbiome samples. Briefly, the microbial peptides obtained from human mcirobiome cells were used for lysine acetylated peptide enrichment using anti-acetyl-lysine (Kac) antibody cocktail; the enriched Kac peptides were then identified and quantified using mass spectrometry.

2020-07-08 | PXD015482 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data